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PubMed1990

[A new method to study behavioral categories and systems of interaction of young children. Initial data].

In the first part of this paper we report on a new method we have developed for the study of the genesis and regulations of the behavior of infants in interactive situations. Detailed information is given on the following aspects: 1. The technical characteristics of the device that allows the infants to be seated in an upright position; 2. The different periods of the experimental procedure; 3. The method used for analyzing the behavioral data. As infants were video-taped without any interruption (real-time record), the behavioral data were analysed in two different ways: A. Macroscopic analyses were carried out using 84 items and 12 categories of behavior. These analyses allowed us to measure the temporal evolution of a limited set of easily recognized behaviors from one experimental period to the next and one experimental session to the next at one-week time intervals; B. Microscopic analyses were carried out with a special software program (THEME) using 222 items divided among 14 categories of behavior. This program was created by Magnusson. It allows the worker to search for significant patterns in sequential events which are recorded in real time, i.e. intra-individual behavioral structure as well as interindividual relationship (interaction). Information is given on the theoretical model and the pattern identification method. The first data can be thus summarized: 1. Four month old infants show a high level competence in their visual attention span in relation to each other; 2. They appear to have varied and complex behavior and interaction processes; 3. Each child has his or her own behavior dynamics throughout each experimental session and from one period to the next; 4. There are some special relationships between infant-infant interactions and the modalities of interaction between each infant and its mother; 5. Periodical behavioral "outbursts" are observed, which might in themselves constitute organizers of behavior; 6. It also makes clear the existence and structure of significant intra- and inter-individual behavioral patterns some of which are particularly complex (patterns are defined as significant connections between two items at least, within a critical time interval, calculated by THEME); 7. It reveals the function of these patterns in mutual adjustment processes between both infants throughout the experimental session.

Attention↗

PubMed1999

Molecular clock mirages.

The hypothesis of the molecular clock proposes that molecular evolution occurs at rates that persist through time and across lineages, for a given gene. The neutral theory of molecular evolution predicts that the clock will be a Poisson process, with equal mean and variance. Experimental data have shown that the variance is typically larger than the mean. Hypotheses have been advanced to account for the hypervariance of molecular evolution. Four recent papers show that none of the predictive hypotheses that have been proposed can be generally maintained. The conclusion is that molecular evolution is dependent on the fickle process of natural selection. But it is a time-dependent process, so that accumulation of empirical data often yields an approximate clock, as a consequence of the expected convergence of large numbers.

Animals↗

PubMed2007

The ongoing adaptive evolution of ASPM and Microcephalin is not explained by increased intelligence.

Recent studies have made great strides towards identifying putative genetic events underlying the evolution of the human brain and its emergent cognitive capacities. One of the most intriguing findings is the recurrent identification of adaptive evolution in genes associated with primary microcephaly, a developmental disorder characterized by severe reduction in brain size and intelligence, reminiscent of the early hominid condition. This has led to the hypothesis that the adaptive evolution of these genes has contributed to the emergence of modern human cognition. As with other candidate loci, however, this hypothesis remains speculative due to the current lack of methodologies for characterizing the evolutionary function of these genes in humans. Two primary microcephaly genes, ASPM and Microcephalin, have been implicated not only in the adaptive evolution of the lineage leading to humans, but in ongoing selective sweeps in modern humans as well. The presence of both the putatively adaptive and neutral alleles at these loci provides a unique opportunity for using normal trait variation within humans to test the hypothesis that the recent selective sweeps are driven by an advantage in cognitive abilities. Here, we report a large-scale association study between the adaptive alleles of these genes and normal variation in several measures of IQ. Five independent samples were used, totaling 2393 subjects, including both family-based and population-based datasets. Our overall findings do not support a detectable association between the recent adaptive evolution of either ASPM or Microcephalin and changes in IQ. As we enter the post-genomic era, with the number of candidate loci underlying human evolution growing rapidly, our findings highlight the importance of direct experimental validation in elucidating their evolutionary role in shaping the human phenotype.

Adolescent↗

PubMed1989

Gene flow by pollen into small populations: Data from experimental and natural stands of wild radish.

Gene flow can have an especially strong impact on the evolution of small populations. However, empirical studies on the actual rates and patterns of gene flow into small populations are few. Thus, we sought to measure gene flow into small populations of wild radish. Raphanus sativus. We found significant differences in gene flow receipt among experimental populations and within those populations over a season. A maximum-likelihood estimate revealed that almost all of the gene flow into these synthetic populations had its origin in relatively distant (>650 m), large natural populations rather than the proximal (255-400 m), small synthetic populations. We also estimated rates of interpopulation mating from simple paternity analysis of progeny produced by seven small (ca. 50 plants) natural populations. Again, we found significant heterogeneity in gene flow receipt. Although these populations varied 10-fold in their range of isolation distances (100-1000 m), gene flow rates did not vary with distance. The magnitude of gene flow rates estimated in all but one population was great enough for gene flow to play an important role in the evolution of these small populations.

Journal Article↗

PubMed2005

Parasites affect song complexity and neural development in a songbird.

There is now considerable evidence that female choice drives the evolution of song complexity in many songbird species. However, the underlying basis for such choice remains controversial. The developmental stress hypothesis suggests that early developmental conditions can mediate adult song complexity by perturbing investment in the underlying brain nuclei during their initial growth. Here, we show that adult male canaries (Serinus canaria), infected with malaria (Plasmodium relictum) as juveniles, develop simpler songs as adults compared to uninfected individuals, and exhibit reduced development of the high vocal centre (HVC) song nucleus in the brain. Our results show how developmental stress not only affects the expression of a sexually selected male trait, but also the structure of the underlying song control pathway in the brain, providing a direct link between brain and behaviour. This novel experimental evidence tests both proximate and ultimate reasons for the evolution of complex songs and supports the Hamilton-Zuk hypothesis of parasite-mediated sexual selection. Together, these results propose how developmental costs may help to explain the evolution of honest advertising in the complex songs of birds.

Animals↗

PubMed2005

Did internal transport, rather than directed locomotion, favor the evolution of bilateral symmetry in animals?

The standard explanation for the origin of bilateral symmetry is that it conferred an advantage over radial symmetry for directed locomotion. However, recent developmental and phylogenetic studies suggest that bilateral symmetry may have evolved in a sessile benthic animal, predating the origin of directed locomotion. An evolutionarily feasible alternative explanation is that bilateral symmetry evolved to improve the efficiency of internal circulation by affecting the compartmentalization of the gut and the location of major ciliary tracts. This functional design principle is illustrated best by the phylum Cnidaria where symmetry varies from radial to tetraradial, biradial and bilateral. In the Cnidaria, bilateral symmetry is manifest most strongly in the internal anatomy and the disposition of ciliary tracts. Furthermore, the bilaterally symmetrical Cnidaria are typically sessile and, in those bilaterally symmetrical cnidarians that undergo directed locomotion, the secondary body axis does not bear a consistent orientation to the direction of locomotion as it typically does in Bilateria. Within the Cnidaria, the hypothesized advantage of bilateral symmetry for internal circulation can be tested by experimental analysis and computer modeling of fluid mechanics. The developmental evolution of symmetry within the Cnidaria can be further explored through comparative gene expression studies among species whose symmetry varies.

Animals↗

PubMed2002

Electrochemical oxidation of phenol at boron-doped diamond electrode. Application to electro-organic synthesis and wastewater treatment.

The electrochemical behaviour of a synthetic boron-doped diamond thin film electrode (BDD) has been studied in acid media containing phenol using cyclic voltammetry and bulk electrolysis. The results have shown that in the potential region of water stability direct electron transfers can occur on BDD surface resulting in electrode fouling due to the formation of a polymeric film on its surface. During electrolysis in the potential region of oxygen evolution, complex oxidation reactions can take place due to electrogenerated hydroxyl radicals. Electrode fouling is inhibited under these conditions. Depending on the experimental conditions, the electrogenerated hydroxyl radicals can lead to the combustion of phenol or to the selective oxidation of phenol to benzoquinone. The experimental results have also been compared to a theoretical model that permits the prediction of the evolution with time of phenol concentration, during its combustion, or during its selective oxidation to benzoquinone.

Benzoquinones↗

PubMed2005

New fluorescence markers to distinguish co-infecting Trypanosoma brucei strains in experimental multiple infections.

Multiple-genotype infections are increasingly recognized as important factors in disease evolution, parasite transmission dynamics, and the evolution of drug resistance. However, the distinction of co-infecting parasite genotypes and the tracking of their dynamics have been difficult with traditional methods based on various genotyping techniques, leaving most questions unaddressed. Here we report new fluorescence markers of various colours that are inserted into the genome of Trypanosoma brucei to phenotypically label live parasites of all life cycle stages. If different parasite strains are labelled with different colours they can be easily distinguished from each other in experimental studies. A total of 10 T. brucei strains were successfully transfected with different fluorescence markers and were monitored in culture, tsetse flies and mice, to demonstrate stability of marker expression. The use of fluorescence activated cell sorting (FACS) allowed rapid and accurate identification of parasite strains labelled with different markers. Cell counts by FACS were virtually identical to counts by traditional microscopy (n=75, Spearman's rho: 0.91, p<0.0001) but were considerably faster and had a significantly lower sampling error (66% lower, d.f.=73, t=-17.1, p<0.0001). Co-infecting strains transfected with fluorescence genes of different colour were easily distinguished by eye and their relative and absolute densities were reliably counted by FACS in experimental multiple infections in mice. Since the FACS can simultaneously determine the population sizes of differently labelled T. brucei strains or subspecies it allows detailed and efficient tracking of multiple-genotype infections within a single host or vector individual, enabling more powerful studies on parasite dynamics. In addition, it also provides a simple way to separate genotypes after experimental mixed infections, to measure responses of the single strains to an applied treatment, thus eliminating the need for laborious cloning steps. The markers presented broaden the spectrum of tools available for experimental studies on multiple-genotype infections. They are fundamentally different from isoenzyme analysis and other genotyping approaches in that they allow the distinction of parasite genotypes based on an easily recognizable phenotypic trait. They will be of specific interest to researches addressing ecological, evolutionary and epidemiological questions using trypanosomes as an experimental system.

Animals↗

PubMed2003

Theoretical investigation of infrared spectra and pocket dynamics of photodissociated carbonmonoxy myoglobin.

Molecular dynamics simulations of the photodissociated state of carbonmonoxy myoglobin (MbCO) are presented using a fluctuating charge model for CO. A new three-point charge model is fitted to high-level ab initio calculations of the dipole and quadrupole moment functions taken from the literature. The infrared spectrum of the CO molecule in the heme pocket is calculated using the dipole moment time autocorrelation function and shows good agreement with experiment. In particular, the new model reproduces the experimentally observed splitting of the CO absorption spectrum. The splitting of 3-7 cm(-1) (compared to the experimental value of 10 cm(-1)) can be directly attributed to the two possible orientations of CO within the docking site at the edge of the distal heme pocket (the B states), as previously suggested on the basis of experimental femtosecond time-resolved infrared studies. Further information on the time evolution of the position and orientation of the CO molecule is obtained and analyzed. The calculated difference in the free energy between the two possible orientations (Fe...CO and Fe...OC) is 0.3 kcal mol(-1) and agrees well with the experimentally estimated value of 0.29 kcal mol(-1). A comparison of the new fluctuating charge model with an established fixed charge model reveals some differences that may be critical for the correct prediction of the infrared spectrum and energy barriers. The photodissociation of CO from the myoglobin mutant L29F using the new model shows rapid escape of CO from the distal heme pocket, in good agreement with recent experimental data. The effect of the protein environment on the multipole moments of the CO ligand is investigated and taken into account in a refined model. Molecular dynamics simulations with this refined model are in agreement with the calculations based on the gas-phase model. However, it is demonstrated that even small changes in the electrostatics of CO alter the details of the dynamics.

Binding Sites↗

PubMed2002

Pattern dynamics of vortex ripples in sand: nonlinear modeling and experimental validation.

Vortex ripples in sand are studied experimentally in a one-dimensional setup with periodic boundary conditions. The nonlinear evolution, far from the onset of instability, is analyzed in the framework of a simple model developed for homogeneous patterns. The interaction function describing the mass transport between neighboring ripples is extracted from experimental runs using a recently proposed method for data analysis, and the predictions of the model are compared to the experiment. An analytic explanation of the wavelength selection mechanism in the model is provided, and the width of the stable band of ripples is measured.

Journal Article↗

PubMed2002

Atomistic mechanisms governing elastic limit and incipient plasticity in crystals.

Nanometre-scale contact experiments and simulations demonstrate the potential to probe incipient plasticity--the onset of permanent deformation--in crystals. Such studies also point to the need for an understanding of the mechanisms governing defect nucleation in a broad range of fields and applications. Here we present a fundamental framework for describing incipient plasticity that combines results of atomistic and finite-element modelling, theoretical concepts of structural stability at finite strain, and experimental analysis. We quantify two key features of the nucleation and subsequent evolution of defects. A position-sensitive criterion based on elastic stability determines the location and character of homogeneously nucleated defects. We validate this stability criterion at both the atomistic and the continuum levels. We then propose a detailed interpretation of the experimentally observed sequence of displacement bursts to elucidate the role of secondary defect sources operating locally at stress levels considerably smaller than the ideal strength required for homogeneous nucleation. These findings provide a self-consistent explanation of the discontinuous elastic plastic response in nanoindentation measurements, and a guide to fundamental studies across many disciplines that seek to quantify and predict the initiation and early stages of plasticity.

Journal Article↗

PubMed2002

Functional substitution for TAF(II)250 by a retroposed homolog that is expressed in human spermatogenesis.

TAF(II)250, the largest subunit of the general transcription factor TFIID, is expressed from the human X chromosome, at least in somatic cells. In male meiosis, however, the sex chromosomes are transcriptionally silenced, while the autosomes remain active. How then are protein-encoding genes transcribed during human male meiosis? Here we present a novel autosomal human gene, TAF1L, which is homologous to TAF(II)250 and is expressed specifically in the testis, apparently in germ cells. We hypothesize that during male meiosis, transcription of protein-encoding genes relies upon TAF1L as a functional substitute for TAF(II)250. Like TAF(II)250, the human TAF1L protein can bind directly to TATA-binding protein, an essential component of TFIID. Most importantly, transfection with human TAF1L rescued the temperature-sensitive lethality of a hamster cell line mutant in TAF(II)250. TAF1L lacks introns and evidently arose by retroposition of a processed TAF(II)250 mRNA during primate evolution. The observation that TAF1L can functionally replace TAF(II)250 provides experimental support for the hypothesis that during male meiosis, autosomes provide cellular functions usually supplied by the X chromosome in somatic cells.

Evolution, Molecular↗

PubMed2004

Spreading of a thin two-dimensional strip of fluid on a vertical plane: experiments and modeling.

We study the thin-film flow of a constant volume of silicon oil (polydymethilsiloxane) spreading down a vertical glass plate. The initial condition is generated from a horizontal fluid filament of typical diameter 0.4 mm. Two optical diagnostic methods are used: One based on an anamorphic system, and the other on the Schlieren method. The first one allows for a detailed characterization of the early stable stage of the spreading which is used to estimate the thickness of the precursor film needed to model the flow. The second one captures the bidimensional pattern of the transversal film instability. We use these techniques to determine the film thickness profiles, and the evolution of the moving contact line, including its shape and Fourier spectra. The numerical simulations of the stable stage of spreading are in good quantitative agreement with the experimental results. We develop a model based on linear stability theory that predicts the evolution of the modes present in the linear stage of the instability.

Journal Article↗

PubMed1985

Evolution as a collective phenomenon.

The quantum mechanical description of biosystems, which emphasise their dielectric properties and the presence of an uncorrelated condensate of phonons, (in analogy with Bose-Einstein condensation), is extended to a description of biosystems, in which the condensed phonons show anomalous averages, (in analogy with superconductivity). The theory is used to show that a quantum ultraviolet defence mechanism may have been present at the origin of chemical evolution, removing a difficulty in the standard scenario. Suggestions are made as to how to proceed experimentally to show the existence of a correlated phonon condensate.

Biological Evolution↗

PubMed2006

Costly punishment across human societies.

Recent behavioral experiments aimed at understanding the evolutionary foundations of human cooperation have suggested that a willingness to engage in costly punishment, even in one-shot situations, may be part of human psychology and a key element in understanding our sociality. However, because most experiments have been confined to students in industrialized societies, generalizations of these insights to the species have necessarily been tentative. Here, experimental results from 15 diverse populations show that (i) all populations demonstrate some willingness to administer costly punishment as unequal behavior increases, (ii) the magnitude of this punishment varies substantially across populations, and (iii) costly punishment positively covaries with altruistic behavior across populations. These findings are consistent with models of the gene-culture coevolution of human altruism and further sharpen what any theory of human cooperation needs to explain.

Africa↗

PubMed2003

Aggregation kinetics of polymer colloids in reaction limited regime: experiments and simulations.

The kinetics of reaction-limited cluster aggregation of fluorinated polymer colloids in a broad range of particle volume fractions has been investigated experimentally by measuring independently the Fuchs stability ratio W and the time evolution of both the average radius of gyration and the average hydrodynamic radius of the aggregates mass distribution. The W value is determined from the aggregation rate at the very initial stage of the aggregation, where the presence of triplets is negligible. The time evolutions of and are then simulated using the cluster mass distribution calculated from the population balance equations with various aggregation kernels proposed in the literature. It is found that, when the measured W value is used, the only kernels that can correctly simulate the experimental results are the product kernel and the one derived by Odriozola et al. (Europhys. Lett. 53 (2001) 797), with some proper tuning of the exponent in the kernel. For the particle volume fraction phi<1%, the obtained value for the exponent is 0.4 and independent of phi, while it tends to decrease for larger phi values, most likely indicating a significant effect of multi-body interactions on the aggregation kinetics.

Journal Article↗

PubMed1999

Functional genomics and enzyme evolution. Homologous and analogous enzymes encoded in microbial genomes.

Computational analysis of complete genomes, followed by experimental testing of emerging hypotheses--the area of research often referred to as 'functional genomics'--aims at deciphering the wealth of information contained in genome sequences and at using it to improve our understanding of the mechanisms of cell function. This review centers on the recent progress in the genome analysis with special emphasis on the new insights in enzyme evolution. Standard methods of predicting functions for new proteins are listed and the common errors in their application are discussed. A new method of improving the functional predictions is introduced, based on a phylogenetic approach to functional prediction, as implemented in the recently constructed Clusters of Orthologous Groups (COG) database (available at http:@www.ncbi.nlm.nih.gov/COG). This approach provides a convenient way to characterize the protein families (and metabolic pathways) that are present or absent in any given organism. Comparative analysis of microbial genomes based on this approach shows that metabolic diversity generally correlates with the genome size-parasitic bacteria code for fewer enzymes and lesser number of metabolic pathways than their free-living relatives. Comparison of different genomes reveals another evolutionary trend, the non-orthologous gene displacement of some enzymes by unrelated proteins with the same cellular function. An examination of the phylogenetic distribution of such cases provides new clues to the problems of biochemical evolution, including evolution of glycolysis and the TCA cycle.

Databases, Factual↗

PubMed1999

Evolution of an integrated HIS in The Netherlands.

This article considers the 26 years history of an integrated hospital information system (HIS). The system emerged from an experimental government sponsored project in the Leiden University Hospital and is now the leading HIS in The Netherlands. The evolution during these 26 years is presented and discussed in this article with an emphasis on the organisational setting and financing besides the aspects functionality, technology/architecture and evaluation aspects. Recently HISCOM was acquired by the BAAN-group completing the evolution and bringing the HIS to the international health care IT market.

Computer Communication Networks↗